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In previous work, structure-based functional site descriptors, fuzzy functional forms (FFFs), were developed to recognize structurally conserved active sites in proteins. These descriptors identify members of protein families according to active-site structural similarity, rather than overall sequence or structure similarity. FFFs are defined by a minimal number of highly conserved residues and their...
The increasing amount of data produced by large-scale biological experiments has highlighted the inadequacies of traditional scientific data management methods such as laboratory notebooks. Databases designed to store biological information are becoming increasingly common, but there is little guidance in the literature about the best practices of biological database design. This paper suggests best...
The growing database of three-dimensional structures of EF-hand calcium-binding proteins is revealing a previously unrecognized variability in the coformations and organizations of EF-hand binding motifs. The structures of twelve different EF-hand proteins for which coordinates are publicly available are discussed and related to their respective biological and biophysical properties. The classical...
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